I don't think they really go over and plan things out on Rifftrax, more like they all watch the movie seperately, write some jokes and then do a viewing to record. I remember reading somewhere that they'd watch the MST3K movies way too many times, especially after The Sidehackers incident. Plus they'd film it.
Mike is better imo in the Rifftrax with Bill and Kevin, and I think that's why they started to be brought on more than originally. (Even just one of them to play off of does wonders.)